RNA-seq analysis of apical meristem reveals integrative regulatory network of ROS and chilling potentially related to flowering in Litchi chinensis

Recently, we documented a hematopoietic NKL-code mapping physiological expression patterns of NKL homeobox genes in human myelopoiesis including monocytes and their derived dendritic cells (DCs). Here, we enlarge this map to include normal NKL homeobox gene expressions in progenitor-derived DCs. Analysis of public gene expression profiling and RNA-seq datasets containing plasmacytoid and conventional dendritic cells (pDC and cDC) demonstrated HHEX activity in both entities while cDCs additionally expressed VENTX. The consequent aim of our study was to examine regulation and function of VENTX in DCs. We compared profiling data of VENTX-positive cDC and monocytes with VENTX-negative pDC and common myeloid progenitor entities and revealed several differentially expressed genes encoding transcription factors and pathway components, representing potential VENTX regulators. Screening of RNA-seq data for 100 leukemia/lymphoma cell lines identified prominent VENTX expression in an acute myelomonocytic leukemia cell line, MUTZ-3 containing inv(3)(q21q26) and t(12;22)(p13;q11) and representing a model for DC differentiation studies. Furthermore, extended gene analyses indicated that MUTZ-3 is associated with the subtype cDC2. In addition to analysis of public chromatin immune-precipitation data, subsequent knockdown experiments and modulations of signaling pathways in MUTZ-3 and control cell lines confirmed identified candidate transcription factors CEBPB, ETV6, EVI1, GATA2, IRF2, MN1, SPIB, and SPI1 and the CSF-, NOTCH-, and TNFa-pathways as VENTX regulators. Live-cell imaging analyses of MUTZ-3 cells treated for VENTX knockdown excluded impacts on apoptosis or induced alteration of differentiation-associated cell morphology. In contrast, target gene analysis performed by expression profiling of knockdown-treated MUTZ-3 cells revealed VENTX-mediated activation of several cDC-specific genes including CSFR1, EGR2, and MIR10A and inhibition of pDC-specific genes like RUNX2. Taken together, we added NKL homeobox gene activities for progenitor-derived DCs to the NKL-code, showing that VENTX is expressed in cDCs but not in pDCs and forms part of a cDC-specific gene regulatory network operating in DC differentiation and function.

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Construction of an lncRNA–mRNA Co-Expression Regulatory Network Mediating Inflammation and Regeneration Following Acute Pancreatitis Injury

10.21203/rs.3.rs-1152574/v1 ◽

2021 ◽

Author(s):

Jing Wang ◽

Tianjie Chen ◽

Xiaohua Zhang ◽

Shulei Zhao

Keyword(s):

Acute Pancreatitis ◽

Mrna Expression ◽

Regulatory Network ◽

Noncoding Rnas ◽

Pancreatic Injury ◽

Control Group ◽

Rna Seq ◽

Damage Repair ◽

Injury And Repair ◽

And Function

Abstract Long noncoding RNAs (lncRNAs) play important roles in the occurrence and development of many diseases and can be used as targets for diagnosis and treatment. However, the expression and function of lncRNAs in the injury and repair of acute pancreatitis (AP) are unclear. To decipher lncRNAs’ regulatory roles in AP, we reanalyzed an RNA-seq dataset of 24 pancreatic tissues, including those of normal control mice (BL), those 7 days after mild AP (D7), and those 14 days after mild AP (D14). The results showed significant differences in lncRNA and mRNA expression of D7/D14 groups compared with the control group. Co-expression analysis showed that differentially expressed (DE) lncRNAs were closely related to immunity- and inflammation-related pathways by trans-regulating mRNA expression. The lncRNA–mRNA network showed that the lncRNAs Dancer, Gmm20488, Terc, Snhg3, and Snhg20 were significantly correlated with AP pathogenesis. WGCNA and cis regulation analysis also showed that AP repair-associated lncRNAs were correlated with extracellular and inflammation-related genes, which affect the repair and regeneration of pancreatic injury after AP. In conclusion, the systemic dysregulation of lncRNAs is strongly involved in remodeling AP’s gene expression regulatory network, and the lncRNA–mRNA expression network could identify targets for AP treatment and damage repair.

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RNA-seq analysis of an apical meristem time series reveals a critical point in Arabidopsis thaliana flower initiation

BMC Genomics ◽

10.1186/s12864-015-1688-9 ◽

2015 ◽

Vol 16 (1) ◽

Cited By ~ 37

Author(s):

Anna V. Klepikova ◽

Maria D. Logacheva ◽

Sergey E. Dmitriev ◽

Aleksey A. Penin

Keyword(s):

Time Series ◽

Arabidopsis Thaliana ◽

Critical Point ◽

Apical Meristem ◽

Flower Initiation ◽

Rna Seq

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Computational Identification of ceRNA and Reconstruction of ceRNA Regulatory Network Based on RNA-seq and Small RNA-seq Data in Plants

Modeling Transcriptional Regulation - Methods in Molecular Biology ◽

10.1007/978-1-0716-1534-8_17 ◽

2021 ◽

pp. 261-275

Author(s):

Xiangyuan Wan ◽

Ziwen Li

Keyword(s):

Small Rna ◽

Regulatory Network ◽

Rna Seq ◽

Computational Identification

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Differential regulatory network-based quantification and prioritization of key genes underlying cancer drug resistance based on time-course RNA-seq data

PLoS Computational Biology ◽

10.1371/journal.pcbi.1007435 ◽

2019 ◽

Vol 15 (11) ◽

pp. e1007435 ◽

Cited By ~ 2

Author(s):

Jiajun Zhang ◽

Wenbo Zhu ◽

Qianliang Wang ◽

Jiayu Gu ◽

L. Frank Huang ◽

...

Keyword(s):

Drug Resistance ◽

Regulatory Network ◽

Time Course ◽

Cancer Drug ◽

Rna Seq ◽

Cancer Drug Resistance ◽

Key Genes

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Correction: A dynamic genetic-hormonal regulatory network model explains multiple cellular behaviors of the root apical meristem of Arabidopsis thaliana

PLoS Computational Biology ◽

10.1371/journal.pcbi.1007140 ◽

2019 ◽

Vol 15 (6) ◽

pp. e1007140

Author(s):

Keyword(s):

Arabidopsis Thaliana ◽

Network Model ◽

Regulatory Network ◽

Apical Meristem ◽

Root Apical Meristem ◽

Cellular Behaviors

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Differential Expression Profiles of the Transcriptome and miRNA Interactome in Synovial Fibroblasts of Rheumatoid Arthritis Revealed by Next Generation Sequencing

Diagnostics ◽

10.3390/diagnostics9030098 ◽

2019 ◽

Vol 9 (3) ◽

pp. 98

Author(s):

Chia-Chun Tseng ◽

Ling-Yu Wu ◽

Wen-Chan Tsai ◽

Tsan-Teng Ou ◽

Cheng-Chin Wu ◽

...

Keyword(s):

Rheumatoid Arthritis ◽

Differential Expression ◽

Regulatory Network ◽

Functional Annotation ◽

Interaction Analysis ◽

Expression Profiles ◽

Synovial Fibroblasts ◽

Rna Seq ◽

Network Mapping ◽

Generation Sequencing

Using next-generation sequencing to decipher the molecular mechanisms underlying aberrant rheumatoid arthritis synovial fibroblasts (RASF) activation, we performed transcriptome-wide RNA-seq and small RNA-seq on synovial fibroblasts from rheumatoid arthritis (RA) subject and normal donor. Differential expression of mRNA and miRNA was integrated with interaction analysis, functional annotation, regulatory network mapping and experimentally verified miRNA–target interaction data, further validated with microarray expression profiles. In this study, 3049 upregulated mRNA and 3552 downregulated mRNA, together with 50 upregulated miRNA and 35 downregulated miRNA in RASF were identified. Interaction analysis highlighted contribution of miRNA to altered transcriptome. Functional annotation revealed metabolic deregulation and oncogenic signatures of RASF. Regulatory network mapping identified downregulated FOXO1 as master transcription factor resulting in altered transcriptome of RASF. Differential expression in three miRNA and corresponding targets (hsa-miR-31-5p:WASF3, hsa-miR-132-3p:RB1, hsa-miR-29c-3p:COL1A1) were also validated. The interactions of these three miRNA–target genes were experimentally validated with past literature. Our transcriptomic and miRNA interactomic investigation identified gene signatures associated with RASF and revealed the involvement of transcription factors and miRNA in an altered transcriptome. These findings help facilitate our understanding of RA with the hope of serving as a springboard for further discoveries relating to the disease.

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